The purpose of this project is to develop methodology for analyzing molecular population genetic data. We have focused on haplotype analysis and continue to investigate the use of spectral analysis of the pairwise LD matrix to describe haplotype structure for Chromosome 12 data for the HAPMAP project. To improve our understanding of the haplotype structure of genes, we are examining the resequenced data of the Environmental Genome Project (EGP). Using recent EGP data for individuals of known ethnicity, we are studying the performance of LD tag SNPS determined from pooled data.